i am attaching a few more slurm files here from participants who i tried to re-run. got the same error for all, didn’t seem to run at all.

📎 slurm-22522819.out

📎 slurm-22522820.out

📎 slurm-22522821.out

i submitted 14 pipelines using the strategies ryan suggested (i.e. each run its own singularity instance; running on 1 core; and using 2min delays for each instance). this went much more smoothly - only 2 came up with errors, which I am attaching here with teh slurm.out files and the data_config.yml file referenced in the slurm files. any thoughts on what the issues are here? i tried rerunning anyways to see if there was a glitch.

📎 cpac_data_config_2020-11-28T19-09-05Z.yml

📎 slurm-22655737.out

📎 slurm-22655744.out

attached is the zipped crash directory.

1. in addition, for all subjects who did get the full output on their first session, they did not have any output for their second session despite having very lot motion estimates as well. do i need to turn on the longitudinal setting for this to work?

I see ses-2 and ses-3 in the data config files, so I think these sessions are just being blocked by C-PAC crashing/dying before getting to them. You could try running a single post-ses-1 session by providing C-PAC with a --data_config_file with just that session, e.g., sub-181_ses-3.

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        - 0.06
        - 1.1225
        - 0.12
        - 1.1825
        - 0.1775
        - 1.24
        - 0.2375
        - 1.3
        - 0.295
        - 1.36
        - 0.355
        - 1.4175
        - 0.415
        - 1.4775
        - 0.4725
        - 1.535
        - 0.5325
        - 1.595
        - 0.59
        - 1.655
        - 0.65
        - 1.7125
        - 0.71
        - 1.7725
        - 0.7675
        - 1.83
        - 0.8275
        - 1.89
        - 0.8875
        - 1.95
        - 0.945
        SoftwareVersions: !!binary |
          c3luZ29fTVJfQjE3
        SpacingBetweenSlices: 4
        StationName: !!binary |
          TUVEUEM=
        TaskName: !!binary |
          cmV3YXYx
        TotalReadoutTime: 0.024885
        TxRefAmp: 383.904
    rewav_run-2:
      scan: /bids_dataset/sub-181/ses-3/func/sub-181_ses-3_task-rewav_run-2_bold.nii.gz
      scan_parameters:
        AcquisitionMatrixPE: 64
        AcquisitionNumber: 1
        AcquisitionTime: !!binary |
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        BandwidthPerPixelPhaseEncode: 39.557
        BaseResolution: 64
        ConversionSoftware: !!binary |
          ZGNtMm5paXg=
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          djEuMC4yMDE4MDYyMiBHQ0M0LjguMg==
        DerivedVendorReportedEchoSpacing: 0.000789999
        DeviceSerialNumber: !!binary |
          MzU0MjY=
        DwellTime: 5.5e-06
        EchoTime: 0.03
        EffectiveEchoSpacing: 0.000395
        FlipAngle: 76
        ImageOrientationPatientDICOM:
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        ImageType:
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        InPlanePhaseEncodingDirectionDICOM: !!binary |
          Q09M
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          V2VzdHdvb2RfQmx2ZF83NDBfTG9zX0FuZ2VsZXNfNTk2NGZlX2VlMjJmODZhZGMyNzk1XzZlMTNk
          M2Y1ZjRj
        InstitutionName: !!binary |
          VUNMQV9Qc3ljaG9sb2d5Xy1fUHN5Y2hpYXRyeQ==
        InstitutionalDepartmentName: !!binary |
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        MRAcquisitionType: !!binary |
          MkQ=
        MagneticFieldStrength: 3
        Manufacturer: !!binary |
          U2llbWVucw==
        ManufacturersModelName: !!binary |
          VHJpb1RpbQ==
        Modality: !!binary |
          TVI=
        ParallelReductionFactorInPlane: 2
        PartialFourier: 1
        PatientPosition: !!binary |
          SEZT
        PercentPhaseFOV: 100
        PhaseEncodingDirection: !!binary |
          ai0=
        PhaseEncodingSteps: 63
        PhaseResolution: 1
        PixelBandwidth: 1420
        ProcedureStepDescription: !!binary |
          VE9UVEVOSEFNX1BBQw==
        PulseSequenceDetails: !!binary |
          JVNpZW1lbnNTZXElX2VwMmRfYm9sZA==
        ReceiveCoilName: !!binary |
          SGVhZE1hdHJpeA==
        ReconMatrixPE: 64
        RepetitionTime: 2
        SAR: 0.160776
        ScanOptions: !!binary |
          RlM=
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          RVA=
        SequenceName: !!binary |
          X2VwZmlkMmQxXzY0
        SequenceVariant: !!binary |
          U0s=
        SeriesDescription: !!binary |
          VGFzazZfUmV3QXZMZWFybmluZ18y
        SeriesNumber: 12
        ShimSetting:
        - 17616
        - -5618
        - 13576
        - 531
        - 138
        - -96
        - 283
        - 17
        SliceThickness: 4
        SliceTiming:
        - 1.005
        - 0
        - 1.0625
        - 0.06
        - 1.1225
        - 0.1175
        - 1.1825
        - 0.1775
        - 1.24
        - 0.2375
        - 1.3
        - 0.295
        - 1.3575
        - 0.355
        - 1.4175
        - 0.415
        - 1.4775
        - 0.4725
        - 1.535
        - 0.5325
        - 1.595
        - 0.59
        - 1.655
        - 0.65
        - 1.7125
        - 0.71
        - 1.7725
        - 0.7675
        - 1.83
        - 0.8275
        - 1.89
        - 0.885
        - 1.95
        - 0.945
        SoftwareVersions: !!binary |
          c3luZ29fTVJfQjE3
        SpacingBetweenSlices: 4
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        TotalReadoutTime: 0.024885
        TxRefAmp: 383.904
    tgng_run-1:
      scan: /bids_dataset/sub-181/ses-3/func/sub-181_ses-3_task-tgng_run-1_bold.nii.gz
      scan_parameters:
        AcquisitionMatrixPE: 64
        AcquisitionNumber: 1
        AcquisitionTime: !!binary |
          MTM6NDE6NTMuNDEwMDAw
        BandwidthPerPixelPhaseEncode: 39.557
        BaseResolution: 64
        ConversionSoftware: !!binary |
          ZGNtMm5paXg=
        ConversionSoftwareVersion: !!binary |
          djEuMC4yMDE4MDYyMiBHQ0M0LjguMg==
        DerivedVendorReportedEchoSpacing: 0.000789999
        DeviceSerialNumber: !!binary |
          MzU0MjY=
        DwellTime: 5.5e-06
        EchoTime: 0.03
        EffectiveEchoSpacing: 0.000395
        FlipAngle: 90
        ImageOrientationPatientDICOM:
        - 1
        - 0
        - 0
        - 0
        - 0.949425
        - -0.313992
        ImageType:
        - ORIGINAL
        - PRIMARY
        - M
        - ND
        - MOSAIC
        InPlanePhaseEncodingDirectionDICOM: !!binary |
          Q09M
        InstitutionAddress: !!binary |
          V2VzdHdvb2RfQmx2ZF83NDBfTG9zX0FuZ2VsZXNfNTk2NGZlX2VlMjJmODZhZGMyNzk1XzZlMTNk
          M2Y1ZjRj
        InstitutionName: !!binary |
          VUNMQV9Qc3ljaG9sb2d5Xy1fUHN5Y2hpYXRyeQ==
        InstitutionalDepartmentName: !!binary |
          TVJJ
        MRAcquisitionType: !!binary |
          MkQ=
        MagneticFieldStrength: 3
        Manufacturer: !!binary |
          U2llbWVucw==
        ManufacturersModelName: !!binary |
          VHJpb1RpbQ==
        Modality: !!binary |
          TVI=
        ParallelReductionFactorInPlane: 2
        PartialFourier: 1
        PatientPosition: !!binary |
          SEZT
        PercentPhaseFOV: 100
        PhaseEncodingDirection: !!binary |
          ai0=
        PhaseEncodingSteps: 63
        PhaseResolution: 1
        PixelBandwidth: 1420
        ProcedureStepDescription: !!binary |
          VE9UVEVOSEFNX1BBQw==
        PulseSequenceDetails: !!binary |
          JVNpZW1lbnNTZXElX2VwMmRfYm9sZA==
        ReceiveCoilName: !!binary |
          SGVhZE1hdHJpeA==
        ReconMatrixPE: 64
        RepetitionTime: 2
        SAR: 0.208512
        ScanOptions: !!binary |
          RlM=
        ScanningSequence: !!binary |
          RVA=
        SequenceName: !!binary |
          X2VwZmlkMmQxXzY0
        SequenceVariant: !!binary |
          U0s=
        SeriesDescription: !!binary |
          VGFzazItVGduZw==
        SeriesNumber: 3
        ShimSetting:
        - 17616
        - -5618
        - 13576
        - 531
        - 138
        - -96
        - 283
        - 17
        SliceThickness: 4
        SliceTiming:
        - 1.005
        - 0
        - 1.0625
        - 0.06
        - 1.1225
        - 0.12
        - 1.1825
        - 0.1775
        - 1.24
        - 0.2375
        - 1.3
        - 0.295
        - 1.36
        - 0.355
        - 1.4175
        - 0.415
        - 1.4775
        - 0.4725
        - 1.535
        - 0.5325
        - 1.595
        - 0.59
        - 1.655
        - 0.65
        - 1.7125
        - 0.71
        - 1.7725
        - 0.7675
        - 1.83
        - 0.8275
        - 1.89
        - 0.8875
        - 1.95
        - 0.945
        SoftwareVersions: !!binary |
          c3luZ29fTVJfQjE3
        SpacingBetweenSlices: 4
        StationName: !!binary |
          TUVEUEM=
        TaskName: !!binary |
          dGduZzE=
        TotalReadoutTime: 0.024885
        TxRefAmp: 383.904
  site_id: site-none
  subject_id: sub-181
  unique_id: ses-3

Crash files with reasons

FileNotFoundError

📎 crash-20201112-221527-av2902-check_func_scan.b7-9537c246-2f20-476d-8ca9-7ba142667aed.pklz

📎 crash-20201112-220558-av2902-select_scan_params.b1-958ca922-e993-42c3-aced-57c4db76ebd5.pklz

📎 crash-20201112-221314-av2902-anat_template_edge_0-03101fbf-8369-4057-9708-df43daac041d.pklz

📎 crash-20201112-221513-av2902-resampled_template_skull_for_anat-21606f07-bee4-4a89-a4eb-84c46095c979.pklz

📎 crash-20201112-221550-av2902-resampled_template_skull_for_func_preproc-f8ab027e-6155-4d08-b66f-aeea8a63f517.pklz

📎 crash-20201112-221529-av2902-selectrest.b4-998f56dc-9a7c-49b5-a610-35dfb87cabba.pklz

📎 crash-20201112-221315-av2902-anat_template_edge_0-4cfa398f-0746-4018-8a6f-36d4bca6d962.pklz

📎 crash-20201112-220558-av2902-check_func_scan.b2-cda0c324-1b35-4f7f-92f1-a0fb43c6eaf2.pklz

📎 crash-20201112-221553-av2902-resampled_template_skull_for_anat-9082064b-aaef-4479-b6ce-2de189a811e7.pklz

📎 crash-20201112-221526-av2902-select_scan_params.b7-9caa04b0-5111-4da8-9d00-b27387e8ad59.pklz

📎 crash-20201112-221517-av2902-resampled_template_brain_for_anat-bdf5bab7-72c0-4893-83a3-da17263a100b.pklz

📎 crash-20201112-220556-av2902-select_scan_params.b4-a4b8846b-91d9-4b22-99c8-daa8b573813f.pklz

📎 crash-20201112-221529-av2902-select_scan_params.b4-3140b40b-e151-4fce-ac92-5067e8877b8e.pklz

📎 crash-20201112-221532-av2902-check_func_scan.b1-0b84fb07-d153-49e0-8943-62f830a7786d.pklz

📎 crash-20201112-221515-av2902-resampled_template_skull_for_anat-974a62b7-3162-4891-9d98-60dbfb14390a.pklz

📎 crash-20201112-221530-av2902-check_func_scan.b3-760e09f1-163f-445d-b9f2-ddf27a39fceb.pklz

📎 crash-20201112-221527-av2902-select_scan_params.b6-50adcc1d-4260-4a58-8f4c-43b203b0ab52.pklz

📎 crash-20201112-221534-av2902-check_for_s3.a1-f13a93ea-5c6d-4d45-a8f9-657771feb81b.pklz

📎 crash-20201112-221259-av2902-lap_tmpl-6cea2816-eca3-43dc-96c3-ee9463bfe78c.pklz

📎 crash-20201112-221304-av2902-lap_tmpl-1950dcd9-381c-41a8-8515-db864a7f96f1.pklz

📎 crash-20201112-220556-av2902-select_scan_params.b4-eddd7b41-dca1-476d-b513-068ce63b1a04.pklz

📎 crash-20201112-220556-av2902-selectrest.b4-56363e91-6774-4f3f-9ede-47491f74ca47.pklz

📎 crash-20201112-220558-av2902-select_scan_params.b2-bc8bc608-6276-4627-807f-d0cedea5a893.pklz

📎 crash-20201112-221539-av2902-lap_tmpl-363cbf2f-65d4-4c06-a9c9-51b95d378023.pklz

📎 crash-20201112-221524-av2902-func_get_idx.b8-da1401b1-67e9-436d-82f7-93ba38731f95.pklz

📎 crash-20201112-221531-av2902-select_scan_params.b2-4e960093-33b1-49fd-9522-d9fb9e26e636.pklz

📎 crash-20201112-221549-av2902-resampled_template_skull_for_func_derivative-6bb749be-1bab-43c0-8721-73841a384ecf.pklz

📎 crash-20201112-221515-av2902-resampled_template_brain_for_anat-a122c362-3a77-46a3-86d8-9d64ffffc80d.pklz

📎 crash-20201112-221524-av2902-func_get_idx.b8-edb2497f-6fc7-46db-8476-7a215dbf6ace.pklz

📎 crash-20201112-221549-av2902-resampled_template_skull_for_func_preproc-d990e452-b918-4f2a-9bd8-af9267ce50dc.pklz

📎 crash-20201112-220557-av2902-select_scan_params.b3-a0a89daf-2aee-47cb-ab8f-f0a4889e8e93.pklz

📎 crash-20201112-221528-av2902-check_func_scan.b6-43fe4cfa-74e7-4415-a567-270a3eececcc.pklz

📎 crash-20201112-221531-av2902-selectrest.b2-3ebcd5e1-1d2b-4d3a-a7f1-5669f8b2ba9b.pklz

📎 crash-20201112-220556-av2902-selectrest.b4-b7833ce1-4cd6-40bb-9586-01870e6f9ba8.pklz

📎 crash-20201112-220557-av2902-selectrest.b3-b598b339-a138-411c-bfb9-86095f27a209.pklz

📎 crash-20201112-221530-av2902-check_func_scan.b3-7796b93f-e8cd-4d85-8232-dc16d6107c5e.pklz

📎 crash-20201112-221529-av2902-select_scan_params.b3-6dfc51af-99f1-411d-9a8e-d71e9e8b70fb.pklz

📎 crash-20201112-221525-av2902-check_func_scan.b8-e80d5b77-4845-4d23-9753-6bfaf4e76e3d.pklz

📎 crash-20201112-221530-av2902-check_for_s3.b3-20a366da-bb5c-451d-a09d-5606b754e8c3.pklz

📎 crash-20201112-221554-av2902-anat_template_edge_0-3207c2f7-5843-422d-ae2f-f04450b1ff48.pklz

📎 crash-20201112-221532-av2902-select_scan_params.b1-4e657ff7-a236-45a1-bb12-86c568604436.pklz

📎 crash-20201112-221525-av2902-sinker_0_raw_functional.b8-d3fc8914-590e-4da7-87a4-812e835bf4a2.pklz

📎 crash-20201112-220557-av2902-check_func_scan.b4-06250430-a644-4cda-b5d6-ae9716a497e3.pklz

📎 crash-20201112-221532-av2902-selectrest.b1-4bb19ae1-ddb5-4908-80ed-c561c8b4d20b.pklz

📎 crash-20201112-221534-av2902-check_for_s3.a0-02d9f09b-3705-456d-a534-e5e80bcd16ab.pklz

📎 crash-20201112-220557-av2902-check_func_scan.b3-3796764b-f33f-4bfd-97b7-e769776ed018.pklz

📎 crash-20201112-221528-av2902-selectrest.b5-d1536989-050e-4304-8a7c-2143a2e8417b.pklz

📎 crash-20201112-221532-av2902-selectrest.b1-698f15c9-eea7-49f8-b361-30c76e975951.pklz

📎 crash-20201112-221531-av2902-selectrest.b2-d7b39c6b-7a78-4a80-864c-d1ad7fa8d8cd.pklz

📎 crash-20201112-221313-av2902-resampled_template_skull_for_anat-5f85e745-6b8f-42d3-941d-9eb820e138be.pklz

📎 crash-20201112-221531-av2902-check_func_scan.b2-97a54684-a9af-446a-a7bb-affbc0323a30.pklz

📎 crash-20201112-221529-av2902-check_func_scan.b4-093fc426-2f93-4825-959c-29c42731462c.pklz

📎 crash-20201112-220558-av2902-check_func_scan.b2-c5685c6b-3d44-4fa6-8de1-18c48222d8dd.pklz

📎 crash-20201112-220557-av2902-check_func_scan.b3-045770fb-5513-489c-8485-63277f569b78.pklz

📎 crash-20201112-221533-av2902-selectrest.b0-2d29da64-fd9b-4de0-a448-87b5d4f6cd43.pklz

📎 crash-20201112-220556-av2902-check_func_scan.b4-637714e9-3fe8-4d01-9b33-06db525822ca.pklz

📎 crash-20201112-221534-av2902-check_for_s3.a0-07a80d16-cbb6-4642-a686-566bde7c572f.pklz

📎 crash-20201112-221555-av2902-anat_template_edge_0-2d2933db-4629-444c-9b55-46982405d5c1.pklz

📎 crash-20201112-221548-av2902-resampled_template_skull_for_func_derivative-7faf7cd8-f8a0-476a-84a7-ea0609268508.pklz

📎 crash-20201112-221526-av2902-check_for_s3.b7-2d078c4e-7134-4c2e-bbde-5a9f7fb02da3.pklz

📎 crash-20201112-221525-av2902-check_func_scan.b8-ad7897ae-a1d8-48d9-935a-93f6a93dbc18.pklz

📎 crash-20201112-221310-av2902-resampled_template_skull_for_anat-7c5afe82-a9f9-4021-aede-def6d25f1240.pklz

📎 crash-20201112-221533-av2902-check_func_scan.b1-a4f55769-6b2a-45aa-bff7-8273c7cac44e.pklz

📎 crash-20201112-221310-av2902-resampled_template_skull_for_func_preproc-859ce541-3d5d-4e18-9907-c6977b8721da.pklz

📎 crash-20201112-221529-av2902-selectrest.b4-f3a3525c-85bd-44a4-8ec2-00776e49b56c.pklz

📎 crash-20201112-220558-av2902-select_scan_params.b2-56b9681b-6399-4b4c-be3c-87e4421ff524.pklz

📎 crash-20201112-221527-av2902-select_scan_params.b6-9e911b35-cdcd-45cb-bf58-4a765e32f161.pklz

📎 crash-20201112-221532-av2902-select_scan_params.b1-26aa62ad-bb89-430f-b9ad-ac6549644387.pklz

📎 crash-20201112-221531-av2902-check_func_scan.b2-40fe4a59-5f18-40d2-ac01-c5cf36d95d9b.pklz

📎 crash-20201112-221531-av2902-select_scan_params.b2-7d6acfb9-e592-4510-a1df-31a2b0e11008.pklz

📎 crash-20201112-221456-av2902-lap_tmpl-76a1462f-3be0-4e5a-9588-180e2fd65129.pklz

📎 crash-20201112-221530-av2902-check_for_s3.b3-6b4c7668-0bf8-4599-bbf6-f557c63ab310.pklz

📎 crash-20201112-221528-av2902-select_scan_params.b5-38d8b4fe-89af-4623-a133-53ae1599e3da.pklz

📎 crash-20201112-221548-av2902-resample_o-142589a2-d388-4425-b6cd-ec04bf1dd8f1.pklz

📎 crash-20201112-221527-av2902-check_func_scan.b7-3fe9020c-c9b0-4209-bb44-5d28971fa04e.pklz

📎 crash-20201112-221309-av2902-resampled_template_skull_for_func_preproc-e987dd6e-f55b-4dd4-a35d-c7189137dc45.pklz

📎 crash-20201112-221525-av2902-sinker_0_raw_functional.b8-dcc67a78-7222-47ad-96a1-8242b82933c9.pklz

📎 crash-20201112-221544-av2902-lap_tmpl-d667fd47-bddf-4296-8776-65c7020565e5.pklz

📎 crash-20201112-221505-av2902-lap_tmpl-22267029-acb1-4a68-80e6-73a7a33f2b7c.pklz

Directory not empty

📎 crash-20201112-221528-av2902-select_scan_params.b4-c3ac09c3-7ffc-4e0d-b072-f67489ba9e03.pklz

📎 crash-20201112-220559-av2902-check_for_s3.b1-0402782f-c3bb-4161-b2c7-9b6857c8ff78.pklz

📎 crash-20201112-221533-av2902-check_func_scan.b0-d411de0f-b4c1-4cb0-aa01-7050b12b25c2.pklz

📎 crash-20201112-221528-av2902-select_scan_params.b5-ea2ac5ac-61c4-4d34-8a0b-83248db84a48.pklz

📎 crash-20201112-221529-av2902-check_func_scan.b4-0997fc0b-2917-4300-81bd-c376d78462ee.pklz

📎 crash-20201112-221533-av2902-select_scan_params.b0-95cba77b-fae9-42ed-b4bf-c9d1315d076e.pklz

📎 crash-20201112-221527-av2902-check_func_scan.b6-643a6816-0e8e-47da-a7af-09b54165d575.pklz

📎 crash-20201112-221527-av2902-selectrest.b6-88e73345-9cbe-4b9d-89a9-4b938fc7fc99.pklz

📎 crash-20201112-220558-av2902-selectrest.b2-89ed0d45-af9e-48e8-a889-53266c1c7861.pklz

📎 crash-20201112-221528-av2902-check_func_scan.b5-f9e1de15-1c2a-40ef-bfdd-be2e4d56ffa9.pklz

📎 crash-20201112-221528-av2902-selectrest.b5-d346b001-545d-4fb8-aabc-521c980e8f2b.pklz

OSError: .proc-* not found

📎 crash-20201112-221527-av2902-selectrest.b6-ba51562a-5103-4f05-9438-8724f88e9ec7.pklz

📎 crash-20201112-220558-av2902-selectrest.b2-2b2da5a9-1594-4dd7-b3a6-cde8a368d367.pklz

📎 crash-20201112-221528-av2902-check_func_scan.b5-80b76d16-b43c-4684-8aa4-294fd683da4d.pklz

📎 crash-20201112-221533-av2902-check_func_scan.b0-051245a2-7e1c-427f-94b9-07b3b089ba7c.pklz

📎 crash-20201112-221533-av2902-select_scan_params.b0-82199afa-6e43-40f7-9066-d8da60d6952e.pklz

📎 crash-20201112-221533-av2902-selectrest.b0-2dc8e5cb-c2b7-4846-aaee-216c585303fb.pklz